As the leader of one of the major supporters of the Confederacy, Hill was a member of the Separatist Council during the Clone Wars, and remained in that position until his assassination at the end of the war.

When economic turbulence erupted across the galaxy as the Separatist Crisis swept through the Galactic Senate, InterGalactic Banking Clan executives profited handsomely from numerous worlds minting their own independent currencies.[7]
When a streak of separatism struck the Galactic Senate, Hill began the search for a new "collections agent" for the Banking Clan who would ensure that despite the turbulent political and economic times, all debts would be paid. Taking note of the world Kalee and the crushing debt it had placed on its shoulders following a Republic embargo on the planet following the Huk War, the Muun Chairman offered to take on the debt and manage to ease the embargo in exchange for the services of KaleeshwarlordQymaen jai Sheelal. Placing Sheelal in command of the Collections and Security Division of the Banking Clan, the Kaleesh eventually left Hill's service to continue fighting for his people on Kalee. Enraged, Hill considered an assassination but refrained in fear of the eventual vengeance of the Kaleesh. Instead he conspired with Poggle the Lesser, the Archduke of Geonosis, and the political idealist CountDooku to arrange Sheelal's permanent servitude. They planted an ion bomb on the warlord's ship, the Martyr, causing it to crash following a fiery explosion. Pulling Sheelal from the wreckage with near-fatal injuries, San Hill funded the construction of the Kaleesh's new cyborg body which would encase his retrievable organs and replace those which could not be saved. In Hill's mind, this monstrosity known as GeneralGrievous would now be capable of defending the IGBC should Dooku's Separatist movement should get out of hand.[5]

As the Clone Wars erupted, Hill was placed on the Confederacy's governing Council, a body which controlled the Confederacy in truth while the Confederacy's Parliament on the planet Raxus debated pointlessly. Despite his pledge of support, Hill was not prepared to commit the entire Banking Clan to the Confederacy with so many profitable investments waiting with the Republic. Retaining their position within the Republic, Hill stayed away from Coruscant while his representatives stayed in the Senate Building. In the early weeks of the Clone Wars, San Hill went to the banking world of Aargau to raise money for the Confederacy of Independent Systems. Navigating the labyrinthine interiors of Aargau's commerce centers, he struck bargains with the criminal underworld to supplement the riches of the Separatists.[12]

In order to secure the Ando system's continued backing, Hill and Wat Tambor appointed former Republic Senator Po Nudo as head of the Hyper-Communications Cartel, the Confederate version of the Republic's HoloNet that used secret Banking Clan codes to spread CIS propaganda. This communications system was used to link the holotransceivers used by many Separatist leaders and keep messages out of the hands of the Republic.[13]

During the Battle of Muunilinst, San Hill commanded the Confederacy forces from a war room atop a large command tower.[14] Hill hid behind the protection of legions of IG lancer droids and the merciless bounty hunterDurge, but the Republic was able to infiltrate his headquarters and bring him, his Banking Clan associates and an Neimoidian aide to trial.[15] Despite his arrest, Hill managed to regain his freedom shortly after and return to the protection of General Grievous.[13]

Despite his escape, Muunilist remained out of Hill's reach after the battle and he was forced to follow the other Councilors around the galaxy in an effort to avoid capture under the protection of Supreme Commander Grievous. Joining the Council aboard the cyborg's flagship, the Invisible Hand, the leadership of the Confederacy was sent to the sinkhole world Utapau to await further instructions. Following Dooku's death over Coruscant at one of the most tumultuous battles of the war, Hill was present with the other Councilors at the meeting during which Grievous ordered them to Mustafar, a mining planet on the Outer Rim where they were promised safety. Not long after departing Utapau, Grievous was killed by Jedi MasterObi-Wan Kenobi, and the Council took full control over the Confederacy.[2]

San Hill gathers around a holotable to receive a message from Darth Sidious.

As the Council arrived on Mustafar, they quickly settled into the dimly lit command center at the mountainside Klegger Corpmining facility. Hill and the other Confederacy leaders were pressed into work at the facility's command center, supervising strategy and battle plans from their remote sanctuary. During their stay, the Council received a communications from the mysterious Darth Sidious, the Confederacy's shadowy benefactor. Sidious promised that the war was over and that the Republic had crumbled under the Separatist's war machine. Advising the Council to remain on the planet, Sidious assured them that he would send his apprentice, Darth Vader, to watch over them. Relieved by the news of victory, Hill and the others anxiously awaited for Vader's arrival and their eventual departure from the inhospitable world. Upon Vader's landing, the Council and its aides gathered in the facility's main command center to greet Vader only to realize soon after he sealed off all of the exits to the facility that he was not there to protect them. Igniting his lightsaber, Vader savagely cut down the guards flanking the doorway before attacking the unarmed Councilors and their aides. Despite Hill's plea for mercy, Vader plunged his lightsaber through the Muun's three hearts, killing him instantly.[16]

San Hill is one of the only Councilors not to receive an onscreen death. The Revenge of the Sith novelization gives a dramatic depiction of San Hill's death; as Darth Vader enters the Separatist command center, Hill rushes to greet the new Sith Lord, saying, "On behalf of the CIS leadership, I would like to be the first to—" To this, Vader sadistically replies, "Very well. You will be the first." When Vader throws back his hood, Hill instantly recognizes him as the former Jedi hero Anakin Skywalker, moments before he is cut down by Vader's lightsaber. The depiction of Hill's death in the Star Wars Episode III: Revenge of the Sith comic is also conflicting with the film depiction, as Hill is struck down alongside both Po Nudo and Poggle the Lesser who die onscreen.

Star Wars: Empire at War: Forces of Corruption introduces another individual named San Hill. Curiously, although this new San Hill is a Human, he bears the same position of Chairman of the InterGalactic Banking Clan and also resides on Muunilinst. Though it seems that both San Hills were meant to be one and the same, this appearance is likely due to a mistake on the part of the game developers.